The difficulties encountered in designing nanoconstructs for medical applications are addressed by developing software for computer-aided design. Our software will be based on a rigorous multiscale analysis to capture both atomic and overall nanosystem features. Broad applicability will be achieved through the use of an interatomic force field within the multiscale framework. Nanoparticle issues we will address include (1) the interaction with selected target diseased cells, (2) thermodynamic stability, (3) unimpeded transport within the circulatory system, (4) timed release of payload therapeutics at diseased tissue, (5) shelf life, and (6) prevention of aggregation. These factors will be addressed across specific ranges of temperature, salinity, and chemical conditions. To accomplish these objectives, a nanosystem simulator, NanoX, will be created to bridge the atomistic and nanostructure scales. A conventional molecular dynamics code cannot simulate these supramillion atom systems over biologically relevant timescales (i.e., milliseconds or longer). We have developed a novel algorithm based on the automated construction of order parameters, which characterizes overall nanoscale features, and a multiscale methodology that enables retention of essential atomistic detail while allowing large spatial and temporal scale computations. We will complete the full implementation of NanoX, test it using data on viral capsids, and demonstrate its capabilities as a computer-aided design tool by using data on liposomes as validation. We will make NanoX freely available as online, open-source software. PUBLIC HEALTH RELEVANCE: Software is developed for designing and analyzing nanoparticles and nanocapsules for applications that include medical imaging and the targeted delivery of therapeutic agents and genes. This software will lead to improved strategies for cancer and gene therapy, refined medical imaging, and the development of magnetic field-guided cancer treatments to the site of the tumor or tissue damage.